Variant Calling

[jerryguintivano]

Hello!

I am working to use rnacocktail to call variants in my data (following alignment using HISAT2). I have run into the following error:

INFO 10:17:19,797 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.8-0-ge9d806836, Compiled 2017/07/28 21:26:50
INFO 10:17:19,797 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute
INFO 10:17:19,797 HelpFormatter - For support and documentation go to https://software.broadinstitute.org/gatk
INFO 10:17:19,797 HelpFormatter - [Thu Feb 14 10:17:19 EST 2019] Executing on Linux 3.10.0-957.el7.x86_64 amd64
INFO 10:17:19,797 HelpFormatter - OpenJDK 64-Bit Server VM 1.8.0_191-b12
INFO 10:17:19,800 HelpFormatter - Program Args: -T HaplotypeCaller -R Homo_sapiens.GRCh37.dna.primary_assembly.fa -I working/gatk/MHXXXXXXX-XXXXXXXXXX/bsqr.bam -o working/gatk/MHXXXXXXX-XXXXXXXXXX/variants.vcf -stand_call_conf 20.000000 -stand_emit_conf 20.000000 -dontUseSoftClippedBases
INFO 10:17:19,808 HelpFormatter - Executing as XXXXXX@XXXXXX on Linux 3.10.0-957.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_191-b12.
INFO 10:17:19,809 HelpFormatter - Date/Time: 2019/02/14 10:17:19
INFO 10:17:19,809 HelpFormatter - ----------------------------------------------------------------------------------
INFO 10:17:19,809 HelpFormatter - ----------------------------------------------------------------------------------

ERROR ------------------------------------------------------------------------------------------

ERROR A USER ERROR has occurred (version 3.8-0-ge9d806836):

ERROR

ERROR This means that one or more arguments or inputs in your command are incorrect.

ERROR The error message below tells you what is the problem.

ERROR

ERROR If the problem is an invalid argument, please check the online documentation guide

ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.

ERROR

ERROR Visit our website and forum for extensive documentation and answers to

ERROR commonly asked questions https://software.broadinstitute.org/gatk

ERROR

ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.

ERROR

ERROR MESSAGE: Invalid command line: The parameter standard_min_confidence_threshold_for_emitting is deprecated. This argument is no longer used in GATK versions 3.7 and newer. Please see the online documentation for the latest usage recommendations.

Does rnacocktail only support GATK version 3.5?

Thanks so much for your help!

[msahraeian]

@jerryguintivano
Happy to see your interest in RNACocktail.
Currently RNACocktail supports GATK 3.5. You can find that version at:
https://software.broadinstitute.org/gatk/download/archive
https://software.broadinstitute.org/gatk/download/auth?package=GATK-archive&version=3.5-0-g36282e4

[msahraeian]

@jerryguintivano
We have upgraded tools to latest version at #17 (GATK 4 is also supported now).
The new docker image (v0.3.0) have these tools pre-installed.